Acquired immunodeficiency syndrome (AIDS) is a serious public health concern. AIDS is caused by Human Immunodeficiency Virus type-1 (HIV-1) which can be subdivided into three highly divergent groups that include: M (main), O (outlier), and N (non-M or O). HIV-1 group M strains are responsible for over 95% of infections worldwide and are further separated into at least nine discreet subtypes or clades (A, B, C, D, F, G, H, J, and K), based on the sequence of complete genomes. Additionally, 13 recombinant forms (CRF) have been characterized that further increase the growing HIV-1 diversity. Overall HIV-1 displays 15-40% nucleotide diversity between subtypes and up to 30% nucleotide diversity within a subtype. Additionally, it has been estimated that there can be between 5 and 10% sequence diversity within an infected individual. In the past few years, HIV-1 research on pathogenesis, replication and host-virus interaction has shifted focus from subtype B laboratory strains to primary HIV-1 isolates of all subtypes. Thus, the heterogeneity of HIV-1 has introduced new challenges for cloning and subsequent functional studies.
Standard molecular biological techniques for manipulation of HIV-1 genetic elements are difficult to apply due to poor sequence conservation between different isolates. Unique restriction endonuclease sites are not conveniently distributed across the HIV-1 genome for selective introduction or mutation of various regions or genes. Additionally, the insertion of new restriction sites for cloning is problematic due to the likely disruption of one or more of the multiple open reading frames found in the virus. As a result, current research on HIV-1 replication relies upon a few closely related molecular clones that have matching restriction endonuclease sites. Alternatively, other methods for studying HIV-1 genes involve trans gene expression with respective deletion in a molecular clone to create pseudotyped viruses. However, these pseudotyped viruses are limited to a single round of replication since the full length functional genome is not packaged in the virus particle.
Treatment of individuals infected with HIV-1 with antiretroviral drugs (ARVs) has changed the face of the AIDS epidemic. Previously, all infection with HIV-1 led to AIDS and mortality in an average of two to seven years. The first anti-HIV-1 ARV, 3′-azido-3′-deoxythymidine (AZT, zidovudine, Retrovir®) was approved in 1987 for therapy but was largely unsuccessful in prolonged treatment due to resistance that develops over time. Until the advent of triple drug combination therapy (Highly Active AntiRetroviral Therapy or HAART), drug resistance was common in all treated patients and remained the primary reason for the failure of ARVs to control HIV viremia. Due to the issues of adherence, the need for lifelong therapy, drug tolerance, and incomplete viral suppression, resistance to ARV still emerges in patients undergoing HAART. Unfortunately, ARV resistance triggers a resumption of disease progression unless new ARVs can be administered in a HAART regimen. Pharmaceutical companies have been successful in continually developing new ARV and in different drug classes.
There are now FDA-approved drugs sub-grouped into three classes of anti-HIV ARVs, which target different steps in the HIV lifecycle: reverse transcriptase inhibitors (RTIs) (nonnucleoside (NNRTI), and nucleoside (NRTI)), protease inhibitors (PRIs), and entry inhibitors (EI) (enfutride, fuseon or T20). Several new HIV-1 entry inhibitors that occlude a viral receptor on the host cells have been effective in pre-clinical development and are now in advanced clinical trials. Additionally, Integrase, another catalytic enzyme of HIV-1 has also been recognized as a rational therapeutic target for the treatment of infection. Integration of the HIV-1 proviral DNA genome into the host genome is essential for viral mRNA transcription but also establishes a stable viral episome in the host genome. Integrase inhibitors and various derivatives could be on the cusp for phase III clinical trials and FDA approval for use in HAART regimens. The continual need for new HIV-1 inhibitors targeting new enzymes or viral processes is due to the emergence of primary resistance to the current PRI and RTIs licensed for therapy. Many of the drug resistant HIV-1 strains selected under a previous regimen also confer cross-resistance to other ARVs in the current FDA-approved arsenal. Cross-resistance limits the use of other drugs in salvage therapy (i.e. following resistance to the first line regimen). Thus, monitoring drug resistance has become a key clinical tool in the management of HIV infected patients by their physicians.
The most basic test for drug resistance is a genotypic drug resistance test which involves sequencing the drug targeted genes PR (encoding protease) and RT (encoding reverse transcriptase) and reporting a predicted resistance pattern. Predicted resistance is based on previous identification of specific resistance mutations and confirmation that these mutations conferred drug resistance in a HIV-1 strain. Since genotypic testing provides only predicted ARV resistance information, many physicians prefer an actual phenotypic drug resistance assay, which involves growing HIV containing patient PR-RT genes in the presence of increasing ARV concentrations. Unlike the multitude of hospital laboratories and companies that perform genotypic drug resistance assays, only two companies offer these HIV phenotypic drug resistance assays, i.e. Monogram Biosciences Inc. (formerly Virologic) and Virco (a division of Johnson & Johnson). These methods employ restriction enzyme cloning, or low efficiency recombination in mammalian cells, respectively. Both methods are very costly and have severe limitations in the ease and adaptability during cloning of patient samples for phenotypic assays. Furthermore, re-development and testing of these phenotypic resistance assays is required to accommodate the new anti-HIV drugs that target other genes or processes (e.g. integration and viral entry) which are now in phase I/II and phase III clinical trials.
A simple sequencing and genotypic analyses is often sufficient to predict resistance due to the relative conservation of HIV-1 PR-RT sequences and well-characterized drug resistance mutations. However, due to the continual emergence of drug resistance, new anti-HIV inhibitors are always needed for effective salvage therapies in patient failing a HAART regimen. Pharmaceutical companies are now pursuing two new classes of ARVs that target the integrase (encoded by IN) and the entry process (involving the env glycoproteins and encoded by the env gene). Several inhibitors are in phase I/II and even phase III clinical trials with a high likelihood of FDA approval within the next two years. Resistance to IN inhibitors appears to be conferred by a distinct set of IN mutations but this data is still very preliminary. In contrast, there is appears to be no distinct pattern of mutations conferring resistance to each entry inhibitor. The env gene is poorly conserved among HIV-1 isolates. Furthermore, there is very large interface between the env gp120/gp41 glycoproteins and the cellular receptors, CD4 and CCR5 (or CXCR4). These two factors contribute to divergent selection of drug resistant mutations which would alter gp120/gp41 structure, transitional rearrangements, and interaction with receptors. Several leading investigators in this field now believe that it may be impossible to predict drug resistance through DNA sequencing/genotype analyses.
Thus, new methods are necessary for cloning into the full HIV-1 genome that also accommodate for the high genetic diversity seen between strains.
Homologous recombination in yeast has been used to clone genes or sequences without the use of restriction endonucleases. However, this cloning technique is unnecessary for most eukaryotic and prokaryotic sequences due to the limited diversity and conservation of sequences cleaved by restriction endonucleases. Yeast gap repair facilitates recombination between a PCR product and a linearized vector via short sequences of comparable homology in both DNA fragments. Selection of the recombined plasmids and their maintenance in yeast is mediated by positive and negative selectable elements within the vector. Finally, these plasmids can be rapidly isolated from yeast and shuttled into E. coli for further subcloning.
The use of a yeast-based recombination method that can be used to clone HIV-1 gag, pol or env sequences of any subtype into a vector for expression in mammalian cells, or for rapid subcloning into a HIV-1 molecular clone has been previously described. The method is not limited by the location of restriction endonuclease sites and holds significant advantages over standard cloning techniques such as: (1) PCR-based TA cloning methods where exogenous sequence must be introduced for subsequent gene expression or subcloning, or (2) PCR-based methods that introduce foreign restriction endonuclease sites by mutating HIV-1 sequence in the primer binding sites. According to that method, an HIV-1 sequence is PCR-amplified and recombined into the vector using a yeast-based recombination system within the proper reading frame, allowing entire genes, gene domains or sub-domains to be studied in context of specific functions. The vector may be transfected into higher eukaryotes for protein expression and functional studies. The HIV-1 genes from this vector can also be shuttled into the infectious HIV-1 molecular clone by classic restriction enzyme/bacterial cloning, which will then provide a vector to produce replication-competent virus in mammalian cells. Unfortunately, the repeated HIV-1 sequences at either end of the genome prevents the use of yeast-based cloning. Yeast simply recombines out the entire HIV-1 coding sequence and generates a non-functional HIV-1 cloning vector.
A need exists for a virus screening system that does not depend on a vector that can recombine to excise virus genes out of the vector and does not depend on the use of restriction endonucleases to create the isolates to be screened.
A need also exists for a method of screening that is not limited to specific genes of the HIV genome. A need further exists for a method of virus screening that can be used to determine susceptibility to various HIV inhibitors, most importantly the entry inhibitors such as CCR5 antagonists. An additional need exists for a method to test susceptibility of viral strains to drugs that target multiple viral constituents.
It is known that as a retrovirus, HIV-1 carries a genome consisting of ribonucleic acid (RNA) rather than deoxyribonucleic acid (DNA). In addition to the same core gene structure shared among all retroviruses (i.e. the gag, pol, and env genes), the HIV-1 genome also harbors several genes found in multiply and singly spliced RNA transcripts (i.e. vif, vpr, tat, rev, vpu, and nef) that encode for several accessory proteins. Replication of the virus after infection of a cell involves reverse transcription of the viral RNA, that is, the creation of a DNA copy of the RNA template. This is accomplished by the enzyme reverse transcriptase. Reverse transcription begins in the primer binding site (pbs) immediately adjacent to one of the two end regions of the linear HIV genome known as the long terminal repeats (or LTRs), specifically the 5′ LTR. The 5′ LTR contains two subregions or segments, the “R” segment, followed by the “U5” segment. The 3′ LTR also contains an R segment, which is identical to the R segment of the 5′ LTR, but the 3′ R segment is preceded by a “U3” segment.
FIG. 1 provides a schematic representation of reverse transcription of a retroviral RNA genome. Reverse transcriptase begins synthesizing a DNA strand from a host tRNALys,3 annealed to the pbs region approximately 100-200 nucleotides from the 5′ end of the viral RNA strand and will proceed to make a DNA copy of the U5 and R RNA segments of the 5′ LTR (termed (−) strand strong stop DNA). When reverse transcriptase makes a DNA copy of all the RNA nucleotides at the 5′ end of the RNA strand, ribonuclease H (RNase H) will degrade the R segment of the viral RNA. The reverse transcriptase will then change templates to the 3′ LTR of the same or a different viral RNA strand. The R segment of the newly synthesized DNA is complementary to and binds to the “R” region of the 3′ LTR of the virus. The DNA segment then acts as a primer for further synthesis of a DNA copy of the viral RNA by reverse transcriptase through the U3 region and then the remainder of the viral genome, resulting in a full length DNA copy of the viral RNA genome. The RNA strand is then degraded by RNase H. Synthesis of a complementary second DNA strand begins at the site denote “PPT.” Strand transfer is also thought to occur with the synthesis of the double stranded DNA.